Genome-wide analysis of inbreeding patterns and candidate genes for adaptation in indigenous chickens of Botswana

Abstract

Indigenous chickens are an important genetic resource in Botswana, providing protein, cultural value and economic benefits to rural communities. The Tswana chicken, comprising multiple strains including Dwarf, Nakedneck, and Normal, has been shaped by domestication, local adaptation and traditional management practices. However, the lack of structured breeding strategies raises concerns about genetic erosion. This study evaluated genomic inbreeding patterns and signatures of selection in Tswana chicken strains using genome-wide SNP data from the 60 K iSelect chicken array. After quality control in PLINK v1.9, 52,719 SNPs from 81 chickens were retained for analysis. Runs of homozygosity (ROH) analysis and complementary selection signature approaches (FST, iHS, Rsb, and xp-EHH) were applied and results revealed generally low levels of inbreeding FROH (Dwarf: 0.01396; Nakedneck: 0.00921; Normal: 0.01216), with most ROH segments being short (<8 Mb).This may indicate that homozygosity largely reflects historical demographic processes rather than recent widespread inbreeding. Long ROH segments were observed only in a subset of Normal individuals, suggesting localized recent relatedness rather than strain-wide effects. A prominent ROH hotspot consistently detected on GGA5 (1.92–3.75 Mb) was shared across all strains and harbored candidate genes including NELL1, ANO5 and SLC17A6 which are implicated in skeletal integrity, neuromuscular function and metabolic processes. In addition, four (4) candidate genes on GGA8 and GGA15 (BRINP3, C1orf21, ISCU, RNF2) were also identified by multiple analytical methods. Collectively, the results indicate low current inbreeding, measurable but moderate population structure and candidate genomic regions potentially associated with adaptation to local production environments. These findings provide a genomic foundation for the sustainable management of Tswana chicken genetic resources.